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Ac update docs #362

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Nov 8, 2017
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ded1e02
Have updated the documenation for using pipelines
Aug 22, 2017
4445d07
I have changed the theme of cgat report to make it easier for the use…
Aug 22, 2017
c359c79
I have made changes to the rst files to increase documentation
Aug 22, 2017
a543ba1
Added extra images to make documentation of pipelines
Aug 22, 2017
5abd060
I have added config for documentation
Aug 23, 2017
1cbe7c8
Have updated some of the documentation as per meeting points
Sep 12, 2017
3a01d98
I have updated some of the documentation
Oct 2, 2017
b1a2440
I have moved some of the prototype pipelines to the obsolete folder
Oct 2, 2017
0d2ae67
I have updated documentation with the new tutorials
Oct 3, 2017
4283462
updated bowtie2 tutorial
Oct 3, 2017
6adb35c
Updated tutorial options
Oct 3, 2017
9313df1
I have added small changes to the docs
Oct 3, 2017
e0ae7b6
Have updated tutorial documentation
Oct 4, 2017
b1bc81b
Have moved PipelineGO because it doesnt seem to be used by any other …
Oct 4, 2017
b0c9cd9
I have also moved PipelineUCSC to obsolete because it seems like it i…
Oct 4, 2017
76fff01
I have removed the PipelineKEGG to obselete because it is only used i…
Oct 4, 2017
d63e6bb
Accidentally moved PipelineUCSC to obsolete, moved back
Oct 4, 2017
c5dc7fe
Have moved metagenome communities pipeline to obsolete as it is a pro…
Oct 4, 2017
c974bec
I have removed the mapping banchmark pipeline to obseolete because it…
Oct 4, 2017
70c5e2d
I have moved pipeline_rnaseqtranscripts to obsolete because it is lis…
Oct 4, 2017
eee8a4f
I have moved prototype pipelines to obsolete
Oct 4, 2017
74f472c
Merge branch 'master' into AC-updateDocs
Oct 4, 2017
c2476ca
I have moved annotations pipeline as this will be releplaced with bam…
Oct 4, 2017
3b70d39
I have updated pipeline_peakcalling documentation
Oct 5, 2017
4cd9183
I have moved some of the pipelines back to the CGATPipelines folder
Oct 9, 2017
772ca74
bamstats tutorial
Oct 17, 2017
98097f8
Updated tutorials with bamstats
Oct 18, 2017
878983b
Merge branch 'master' into AC-updateDocs
Oct 23, 2017
9400e4e
updated report and background docs
Oct 23, 2017
7204b2b
updated report doc
Oct 24, 2017
e0395d8
Merge branch 'master' into AC-updateDocs
Oct 26, 2017
c6dce66
updated tutorial
Oct 26, 2017
d3dc663
More tutorial doc updates
Oct 26, 2017
73168ae
update installation instructions
sebastian-luna-valero Nov 8, 2017
4925842
update installation instructions
sebastian-luna-valero Nov 8, 2017
be480e4
update installation instructions
sebastian-luna-valero Nov 8, 2017
dab033d
update installation instructions
sebastian-luna-valero Nov 8, 2017
c37b5c9
update installation instructions
sebastian-luna-valero Nov 8, 2017
02f1a38
update developers section
sebastian-luna-valero Nov 8, 2017
6d9a881
update pipelines background
sebastian-luna-valero Nov 8, 2017
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update installation instructions
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sebastian-luna-valero committed Nov 8, 2017

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commit 4925842cd1a1de0e55cc20e5fbf7b4a7f7747918
4 changes: 2 additions & 2 deletions doc/InstallingPipelines.rst
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
Installation instructions
=========================

The section below describes how to install the CGAT Pipelines. We distinguish between two
The section below describes how to install the CGAT_ Pipelines. We distinguish between two
different installation types: production and development. The former refers to a well
tested subset of pipelines, and is the recommended installation. The latter refers to
the whole collection of pipelines developed at CGAT, which may contain code under active
@@ -100,4 +100,4 @@ To check if the dependencies within a particular pipeline are satisfied, type::
python CGATPipelines/pipeline_mapping.py --input-validation

.. _conda: https://conda.io

.. _CGAT: http://www.cgat.org